The Paradigm Shift
by TheWabbajackX
Summary: All of reality is at stake when the Doctor becomes involved in a war with a man crazier than he is. His goal: to crush the Doctor completely. He is cruel, intelligent, merciless, and plays dirty. Everything the Doctor knows and loves is in absolute danger. He will be put to the biggest test since the Last great Time War. Will order trump chaos, or is this truly his last stand?
1. Prologue

_A sense of victory and relief washed over the masses after order had been restored to the Library. The sun was setting over the moon, bathing all that was under it in a bronze glow. As the people saved by the system were returning to their homes, none of them knew of the sacrifices that were made today. _

_The Doctor and Donna Noble were standing on a balcony, watching the glow of the sun as it washed over them. They had beaten the Vashta Nerada and restored the library to its former glory, but they felt no sense of triumph within them. Donna's perfect family and world were all a sham. Loneliness hung inside her chest like an anchor. The Doctor was not much better, having just watched River Song sacrifice herself to save the Library. She knew so much about him, even his name, but he knew nothing of her. Deep inside, he knew this would be a mystery that would one day return to him. Yet, this did little to quell the uneasiness he felt. River's tattered and worn diary sat on the railing before the both of them. The TARDIS Blue leather cover seemed to tease and tantalize him with all the mysteries it surely contained in its pages. The Doctor ran his fingers over the rough leather cover. He could feel the age deep in the wrinkles and grooves. Donna and the Doctor gazed at it, fighting any and all temptation to read it._

"_Your friend," Donna spoke up. The Doctor was still fixated on the diary, lost in the maze of "what ifs" that ran through his head. He could see her concerned expression out of his peripheral but didn't turn to face her. "Professor Song." He quickly looked over to his companion, her name snapping him back to reality. The Doctor was quick to notice the concern washed over her face. "She knew you in the future, but she didn't know me. What happens to me?" The Doctor had known her for quite some time now. She was very vocal in anything she had to say. He had never heard her so quiet before. The Doctor wanted to tell her something, anything, to bring some sort of comfort to her. He had no answers to give, and that frightened him. "When she heard my name, the way she looked at me-"_

"_Donna." His eyes went back to the book before them both. "This is her diary." He pushed down on it with his hand. "My future. I could look you up." He couldn't hide the excitement on his face. He tapped the cover with his skinny fingers. "What do you think? Shall we peek at the end?" He stared at the book with a longing hunger and gave Donna a look that said "yes" and "no" all at once. Donna's eyes swapped from the diary to the Doctor. She tapped the bar slowly, mulling it over. _

"_Spoilers, right?" _

"_Right."_

_They both shared relief and disappointment. The two of them were deeply tempted to read it and remove the fog shrouding River Song. Donna had to stick to the Doctor's word and the Doctor on his own. The Doctor was very thankful that she had declined. If she had given him the go ahead, he was unsure if he could have refused. Thankfully, he wouldn't have to find out. The two smiled at one another, taking pride in themselves for refusing the diary. The Doctor removed the old rusty sonic screwdriver from the inner pocket of his trench coat and sat it atop the diary. He sat his hands in his pockets and turned away, his coat whipping through the air as he left the diary and screwdriver behind._

"_Come on. The next chapter's this way." Donna followed him up the steps, eager to leave the Library behind. They did not get far before the Doctor sprinted back to the diary and clutched the old screwdriver in his fingertips, his wild eyes scanning it furiously. "Why? Why would I give her my screwdriver? Why would I do that?" Donna watched him unleash all the energy he had stuffed deep inside of his chest. "Thing is, future me had years to think about it. All those years to think of a way to save her, and what he did was give her a screwdriver. Why would I do that?" A small panel on the side caught his attention. He removed it, finding a neural relay hidden underneath. "Ohhhhhh. Look at that!" The neural relay had a single flickering yellow bar displayed on the digital display. "I'm very good!"_

"_What have you done?" Donna was completely lost._

"_Saved her." His face was alight with energy, his face adorned with that crazy grin Donna was accustomed to seeing. Donna watched his sprint away with the screwdriver in his hands. She had never seen him run so fast before. _

"_Doctor, wait! How did you save her? What are you going to do?" These questions went unanswered as she chased after the Doctor. Their footsteps eventually dissipated into silence, with the diary sitting by itself in the quiet of the Library. The diary would have sat in silence forever, either completely wasting away into nothing, catalogued and stuffed into one of the hundreds of shelves, or blown off the rail and fall down into the city below. All this was prevented thanks to the hand that now touched it. It was a skinny hand covered by a black leather glove. Underneath the glove was pale skin with a huge vein running through the hand. The bones could be seen in the palm. A young man stood on the balcony alone with the diary. He wore a black coat that descended down beyond his feet. The sleeves were long and had red trim at the ends. A large red shell-shaped collar rose behind his head. The young man had sickly yellow eyes and dark brown raggedy hair hanging from his head. He stared at the book before him with an enormous hunger. Gently, he flipped the blue cover over and eyed the words scrawled on the page with a lovely handwriting. A sinister smile crept slowly under his nose._

"_Well, hello, sweetie," he said in a low and gravelly voice._


	2. Young Blood: Part 1

Clara sat in her chair, swinging her legs as she watched her Doctor fiddle with the controls glowing on the console. He was lost in his own little world, his face alight with happiness like a little boy on his birthday. He always had that look when it came to piloting the TARDIS to their next destination, even if he had absolutely no idea what he was doing.

The day had proven to be quite slow for the two of them. They had tea with the Silurian detective Madame Vastra, her wife Jenny Flint, and their butler Strax the Sontaran. Clara found it relaxing and enjoyed catching up with her odd trio of friends, but the Doctor quickly developed cold feet and took her back in the TARDIS to try and find some adventure. They went to the terraformed planet Sauria, an intergalactic park owned by the Silurians to house every species of dinosaur that had existed. They swapped exciting tales with Geoffrey Chaucer, although they couldn't let the man add them to his collection of works he was developing. These were fine for Clara's taste, but the Doctor kept itching for something more exciting. The old blue girl was coming up blank on her end. It was as though all the trouble in the universe decided to take a hiatus for the day.

"Don't fret, Clara," the Doctor consoled. "I'll get us into some trouble soon. Just you wait."

"Don't wear yourself out then," she said nonchalantly. She was glad he had his back to her. Otherwise, she wouldn't be able to hide the small smile on her face. He was trying so hard to find something fun for her. She found it absolutely adorable. In all honestly, however, what she really wanted was to just enjoy this slow day with him. No ghosts, Daleks, Cybermen, or snow monsters. She figured that the two of them could catch a movie or practice baking soufflés. The Doctor was really bad at baking soufflés, but she found his attempts to be so precious. What she wanted was to just hang out. To have a normal day with her friend. Or maybe she wanted a date. A proper date. With her Doctor. A slight blush crept onto her cheeks at the thought. "Doctor?"

"Yes, Clara?" the Doctor asked, not turning to her. He was still flipping switches and cranking pumps like there would be no tomorrow.

"Do you think we could just go back to London?" she asked. He turned to her, a bewildered look on his face. Clara figured she wouldn't have another lazy day opportunity like this to try her luck. "Just hang out and take in the slow day together?"

"Hang out?" he repeated slowly. Clara nodded, a smirk on her face. No matter how human he looked, he was anything but. She found it very charming when he tried to understand human things. "Like…. texting each other and having scones?" Now it was Clara's turn to look bewildered. It wasn't the oddest thing he had ever said, but it was not exactly a combo that made sense.

"Sure, why not?" When it came to the Doctor and social aspects, a bowling ball had a better chance at floating than him doing anything that could even remotely be labeled "normal", but that mattered little to her. She was her Doctor, and she always enjoyed his company, regardless of what they were doing. "Texting and scones." Even after agreeing to the idea, it still sounded incredibly strange to her. The TARDIS grew quiet as it came to a halt.

"Come along, Clara," the Doctor said, shimmying to the doors. They swung open with a creak, and the sunlight poured inside. He peeked out through the doorway, finding they had materialized in the middle of an empty park. The sun was hidden behind the clouds hanging in the sky. Clara gently grasped the Doctor's hand and held him close. The two exchanged warm smiles and skipped out of the TARDIS. The squeal of car tires rang through the air, causing the Doctor and Clara to snap their heads in the direction of a SUV stopped several feet before them. The Doctor squinted to make out the symbol on the front hoods of the SUV. It was a T made out of multiple hexagons. "Torchwood!"

"When did you invite them?"

"I didn't."

Two tall men in black suits and sunglasses stepped out of the SUVs and approached the two of them, flashing their badges.

"This the guy?"

"Blue police box. Has to be."

"Description doesn't match, though."

"He can alter his form, remember?"

"Who's the girl?"

"Doctor predominantly travels with one female companion."

"I have a name, you know," Clara blurted. The two men looked at her awkwardly. "Clara Oswald." The two looked back towards each other.

"Hello! I'm the Doctor!" He waved at them with a smile on his face. The two men raised eyebrows at one another. "To what do I owe this little visit from Torchwood? Oh, good to see you guys back at the top again, by the way. Love the suits. Very men in black."

"We need you to come with us, sir."

"Matter of importance."

"You lot got serious, didn't you? No fun anymore. Jack kept things interesting, at least."

"What's got you two in such a knot?" Clara asked.

"Torchwood was been waiting for the Doctor's return for quite some time now. We need to be….. reacquainted." The Doctor and Clara exchanged concerned glances. The Doctor merely shrugged and sauntered over to the SUV, tapping the hood with the flat of his palm.

"Off we go, then!" The two men in suits strode over to him, with Clara in tow. She slid into the back seat beside the Doctor. The SUV started up and drove down the street. Clara leaned close to the Doctor and whispered to him.

"Doctor, are you sure about this?"

"Absolutely not," he replied. Clara gave him a look, but it didn't register with the Doctor. His head snapped up quickly. "Oh! You're worried."

"Not necessarily," she said. "You've worked with them before, I bet."

"Oh, yes," the Doctor said. "Old friend of mine, Jack Harkness, was quite big among them. They probably just want to catch up. I haven't seen them in….. what year is this?" The man in the passenger seat looked back at them.

"2064, sir." The Doctor and Clara looked surprised.

"Huh. Off by a few decades, but this day needed a little excitement."

"I thought we were gonna text and have scones," Clara said, pretending to pout.

"Oh, we can do all that later. I promise."

* * *

Torchwood Tower stood tall and proud over Canary Wharf. The memory of the battle between the Cybermen and the Daleks from so many years ago seemed like another world to the ordinary citizens. It was still as fresh as the day it happened in the Doctor's mind. That battle had changed the Doctor's life forever. Losing Rose. Meeting Donna. It was hard for him to believe that he was back here, everything looking untouched. The car came to a halt in one of the spaces in the underground parking garage. The Doctor and Clara followed the two men in suits into the elevator. One of them hit a button for one of the higher floors, and the doors slid shut. The four of them stood in silence as the low hum of the elevator resonated as they climbed higher into the building. They eventually came to a stop, and the doors slid open. A grey hallway with several glass windows on the walls stretched out before them. Unbeknownst to the Doctor and Clara, they were being watched by one of the security cameras. It was glued to their every move. The Doctor and Clara took notice of all the unusual things they spotted through the windows. A giant black monolithic slab, particle accelerators, and things that Clara couldn't even begin to describe.

"In this room, please," one of the men in suits said, opening a door for the two of them. A woman was sitting behind a desk with a holographic screen floating before her. The Doctor slid over to one of the chairs and sat in it, with Clara slinking into her seat right beside him.

"Mr. Doctor," she said with a nod.

"Oh, it's just "the Doctor", please," he said with a friendly nod.

"And Clara Oswald." The woman nodded.

"New travelling companion," she noted. "And you, Doctor. Your physical form has changed since your previous association with Torchwood. Now, according to our records, your previous form was your… tenth, correct?" The Doctor tapped slowly on the arm rest of his chair. Clara gave him a concerned look.

"…..Yes. Have you been…. spying on me?"

"Doctor, you have a very comprehensive history throughout our history." She tapped several panels on the holographic interface and pulled up a few digital images of his previous regenerations. "Subtlety is not your strong suit." Clara gasped with excitement and pointed at one of the images.

"I love the scarf!"

"Oh, me too!" the Doctor said. "Despite how good I look, I don't really appreciate being watched."

"Doctor, you've done so much for us," the woman continued. "For both humanity and Torchwood. You're a hero, whether you realize it or not. We collected this record of your actions here on Earth in the event of a repeat incident like the Battle of Canary Wharf. Pardon me. I haven't even given you my name. I am Samantha Pentagast. I'm quite the fan, Doctor."

"Oh, I have fans now," the Doctor said. "Fans are cool." Clara rolled her eyes at him, to which she received a frown from his end.

"Now, Doctor, there's a bit of a gap in our databases on you since our last encounter," Miss Pentagast started. "Do you mind telling us a bit about your endeavors after you had regenerated?"

"Sounds fun, but it might be a while."

"I've got time."

"Oh, I was speaking to Clara." He turned to her. "Go and explore for me, will you? Unless you want to sit here and listen to an old man reminisce?" Clara let out a small laugh.

"I think I'll pass," she said and stood up.

"These two will escort you," Miss Pentagast said, pointing to the two men in suits who replied with silent nods.

"If he starts talking about the fez, stop him," Clara told her.

"Oi!" the Doctor said. "I like that fez. Fezzes are very-"

"Cool. I get it." Clara left the room with the two men in tow.

"We'll show you some of our low-key projects, Miss…. Oswald, was it?" She followed the two of them down the hallway, stopping to watch all the amazing things they were studying. The monolith was quite intriguing, despite looking like a black slab of marble. Her attention was drawn to the vibration her phone gave off. She had just received a text message, but from whom? She removed her phone from her pocket and saw it.

_Hello_.

That was all it said. The number didn't make any sense. 000-000-0000. Clara became a bit worried, remembering when she had become trapped inside the cyber web of London's Wi-Fi. It unnerved her greatly. She would do anything to avoid returning to that dreadful place. However, she remembered how brave the Doctor was. He had saved her. If something were to happen, he would be there to fix it. While this comforted Clara, she did not wish a repeat performance.

"Better play it safe," she said softly.

_Hello :)_

After she sent the message, she kept staring at her phone for any sort of reply. She did not have to wait long.

_Who are you?_

_Clara. Clara Oswald._

_You're really pretty._

A smile accompanied the slight blush on her face. This mystery person sent her another message.

_How did you get here?_

_They brought us here. Who are you?_

What Clara got next chilled her to her bones.

_A prisoner._

The back of her neck grew hot with worry. Her eyes nervously glanced at the two men in suits.

"Ma'am, is something wrong?" one of them asked. She realized something. He had called her "pretty". She quickly texted a reply.

_Can you see us?_

_Look up._

A camera was staring right at her. She quickly stepped to the left, and the camera followed her motions. She stepped to the right, and it followed her there. The two men in suits took notice of the camera.

"Oh no," one of them muttered quietly. "Not again." Clara quickly turned to him.

"Does this happen a lot?" she asked. The man that spoke bit his lip.

"Miss, we've said too much," the other one said. Clara walked quickly back to the room where the Doctor and Miss Pentagast were speaking.

"Wait, she named her daughter after her daughter?"

"It only gets weirder from there." The Doctor turned to her, his smile fading quickly when he saw the concern in her eyes. "Clara, what's wrong, sweetie?" She handed him her phone. The Doctor scrolled through the messages she had received from this mystery number. "Miss Pentagast, do you know what this is about?" He handed her the phone. Upon seeing it, she sighed.

"He's at it again," she said. Miss Pentagast dialed the number from her holographic interface. A tone reverbed for a second before a voice came from the speakers.

"Yes, hello?" a young and agitated male voice asked.

"Why you are harassing this young lady?" Miss Pentagast asked.

"I don't recall authorizing you to contact me directly, Miss Pentagast," the voice said. She was quiet for a second.

"No, sir, you did not."

"Luckily for you, I am feeling charitable," the voice said. "Now, Miss Oswald and the chin guy are in the room with you, correct?"

"Chin guy?" the Doctor asked.

"Watch it," she said between giggles. "You'll poke someone's eye out with that." The Doctor patted his chin.

"Place them on visual," the voice said. Miss Pentagast pushed one of the holographic panels on the interface, and video feed of the room popped up. They turned to the security camera on the wall above them. The Doctor and Clara stared into it. "Mr. Bowtie, I'd like to have a talk with you face to face. If you're who I think you are, we may have much to discuss. Meet me in my office. Alone, please." Clara didn't like the sound of this. The Doctor, however, was very intrigued.

"And where is your office?"

"Miss Pentagast will take you," the voice said. There was a click and then silence.


End file.
